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enhancerHomologSearch

This is the development version of enhancerHomologSearch; for the stable release version, see enhancerHomologSearch.

Identification of putative mammalian orthologs to given enhancer


Bioconductor version: Development (3.19)

Get ENCODE data of enhancer region via H3K4me1 peaks and search homolog regions for given sequences. The candidates of enhancer homolog regions can be filtered by distance to target TSS. The top candidates from human and mouse will be aligned to each other and then exported as multiple alignments with given enhancer.

Author: Jianhong Ou [aut, cre] , Valentina Cigliola [dtc], Kenneth Poss [fnd]

Maintainer: Jianhong Ou <jianhong.ou at duke.edu>

Citation (from within R, enter citation("enhancerHomologSearch")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("enhancerHomologSearch")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("enhancerHomologSearch")
enhancerHomologSearch Vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, GeneRegulation, Sequencing, Software
Version 1.9.4
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL (>= 2)
Depends R (>= 4.1.0), methods
Imports BiocGenerics, Biostrings, BSgenome, BiocParallel, BiocFileCache, GenomeInfoDb, GenomicRanges, httr, IRanges, jsonlite, motifmatchr, Matrix, rtracklayer, Rcpp, S4Vectors, stats, utils
System Requirements
URL https://jianhong.github.io/enhancerHomologSearch
Bug Reports https://github.com/jianhong/enhancerHomologSearch/issues
See More
Suggests knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, MotifDb, testthat, TFBSTools
Linking To Rcpp
Enhances
Depends On Me
Imports Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package enhancerHomologSearch_1.9.4.tar.gz
Windows Binary enhancerHomologSearch_1.9.4.zip
macOS Binary (x86_64) enhancerHomologSearch_1.9.4.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/enhancerHomologSearch
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/enhancerHomologSearch
Bioc Package Browser https://code.bioconductor.org/browse/enhancerHomologSearch/
Package Short Url https://bioconductor.org/packages/enhancerHomologSearch/
Package Downloads Report Download Stats